Starting phenix.real_space_refine on Tue Jul 29 00:15:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k53_36896/07_2025/8k53_36896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k53_36896/07_2025/8k53_36896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2025/8k53_36896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2025/8k53_36896.map" model { file = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2025/8k53_36896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2025/8k53_36896.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6663 2.51 5 N 1852 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5998 Classifications: {'peptide': 777} Link IDs: {'PCIS': 8, 'PTRANS': 48, 'TRANS': 720} Chain: "B" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4439 Classifications: {'peptide': 573} Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.52, per 1000 atoms: 0.71 Number of scatterers: 10602 At special positions: 0 Unit cell: (106.72, 168.36, 207.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2043 8.00 N 1852 7.00 C 6663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 587 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1101 " - " ASN A 76 " " NAG A1102 " - " ASN A 477 " " NAG B1101 " - " ASN B 76 " " NAG C 1 " - " ASN A 461 " " NAG D 1 " - " ASN A 498 " " NAG E 1 " - " ASN B 461 " " NAG F 1 " - " ASN B 498 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.5 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 44 sheets defined 3.0% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.684A pdb=" N LEU A 202 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.863A pdb=" N GLU A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.739A pdb=" N ASP A 482 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 483' Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.118A pdb=" N ALA B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.616A pdb=" N LEU B 202 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.845A pdb=" N GLU B 301 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.596A pdb=" N GLU B 483 " --> pdb=" O ARG B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41 removed outlier: 5.690A pdb=" N GLY A 36 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER A 66 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 62 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.297A pdb=" N VAL A 46 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLY A 130 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 48 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LEU A 132 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 145 removed outlier: 6.277A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 145 removed outlier: 6.277A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA8, first strand: chain 'A' and resid 237 through 243 removed outlier: 5.682A pdb=" N ALA A 238 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASN A 266 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE A 262 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 248 through 252 removed outlier: 6.471A pdb=" N THR A 249 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN A 324 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA A 251 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260 Processing sheet with id=AB2, first strand: chain 'A' and resid 328 through 331 removed outlier: 6.457A pdb=" N ALA A 349 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AB4, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AB5, first strand: chain 'A' and resid 430 through 431 removed outlier: 6.863A pdb=" N ALA A 430 " --> pdb=" O ARG A 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 435 through 438 Processing sheet with id=AB7, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AB8, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.311A pdb=" N HIS A 531 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 518 through 520 removed outlier: 3.615A pdb=" N VAL A 602 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 583 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.687A pdb=" N LEU A 526 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 612 through 617 removed outlier: 3.621A pdb=" N GLY A 612 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 614 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 627 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 616 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN A 625 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.311A pdb=" N VAL A 685 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA A 687 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 663 through 664 removed outlier: 4.671A pdb=" N ILE A 663 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 703 " --> pdb=" O TYR A 681 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AC6, first strand: chain 'A' and resid 759 through 764 removed outlier: 6.437A pdb=" N ILE A 788 " --> pdb=" O GLU A 799 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 799 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N SER A 790 " --> pdb=" O GLY A 797 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 759 through 764 Processing sheet with id=AC8, first strand: chain 'B' and resid 35 through 41 removed outlier: 5.948A pdb=" N GLY B 36 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER B 66 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B 62 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.275A pdb=" N VAL B 46 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY B 130 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE B 48 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LEU B 132 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.504A pdb=" N THR B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.664A pdb=" N VAL B 96 " --> pdb=" O GLN B 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.063A pdb=" N VAL B 143 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.063A pdb=" N VAL B 143 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 151 through 153 Processing sheet with id=AD6, first strand: chain 'B' and resid 237 through 243 removed outlier: 5.571A pdb=" N ALA B 238 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASN B 266 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 262 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 248 through 252 removed outlier: 3.689A pdb=" N ILE B 322 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 248 through 252 removed outlier: 3.689A pdb=" N ILE B 322 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN B 326 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYS B 353 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 349 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 257 through 260 Processing sheet with id=AE1, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.491A pdb=" N THR B 336 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLN B 413 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA B 338 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 343 through 347 Processing sheet with id=AE3, first strand: chain 'B' and resid 415 through 418 removed outlier: 5.513A pdb=" N ALA B 416 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA B 445 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 427 through 431 removed outlier: 7.016A pdb=" N ILE B 428 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ARG B 506 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA B 430 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 436 through 438 Processing sheet with id=AE6, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.196A pdb=" N HIS B 531 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 518 through 521 Processing sheet with id=AE8, first strand: chain 'B' and resid 526 through 528 391 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3525 1.34 - 1.46: 2407 1.46 - 1.58: 4858 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 10854 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" CB PRO B 469 " pdb=" CG PRO B 469 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.56e+00 bond pdb=" C1 NAG B1101 " pdb=" O5 NAG B1101 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 10849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 14382 1.67 - 3.35: 338 3.35 - 5.02: 33 5.02 - 6.69: 16 6.69 - 8.36: 6 Bond angle restraints: 14775 Sorted by residual: angle pdb=" CA PRO B 469 " pdb=" N PRO B 469 " pdb=" CD PRO B 469 " ideal model delta sigma weight residual 112.00 104.14 7.86 1.40e+00 5.10e-01 3.15e+01 angle pdb=" C ASN A 498 " pdb=" CA ASN A 498 " pdb=" CB ASN A 498 " ideal model delta sigma weight residual 109.72 115.30 -5.58 1.61e+00 3.86e-01 1.20e+01 angle pdb=" CA GLN B 318 " pdb=" CB GLN B 318 " pdb=" CG GLN B 318 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CB GLN B 318 " pdb=" CG GLN B 318 " pdb=" CD GLN B 318 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.70e+00 3.46e-01 1.08e+01 angle pdb=" C SER B 86 " pdb=" N ARG B 87 " pdb=" CA ARG B 87 " ideal model delta sigma weight residual 120.99 127.11 -6.12 1.86e+00 2.89e-01 1.08e+01 ... (remaining 14770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 6193 21.45 - 42.90: 415 42.90 - 64.35: 78 64.35 - 85.81: 17 85.81 - 107.26: 6 Dihedral angle restraints: 6709 sinusoidal: 2836 harmonic: 3873 Sorted by residual: dihedral pdb=" CA ALA A 497 " pdb=" C ALA A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TRP A 678 " pdb=" C TRP A 678 " pdb=" N MET A 679 " pdb=" CA MET A 679 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.55 107.26 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 6706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1657 0.151 - 0.301: 7 0.301 - 0.452: 1 0.452 - 0.603: 0 0.603 - 0.753: 1 Chirality restraints: 1666 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 461 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.81 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1663 not shown) Planarity restraints: 1937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 468 " -0.071 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 469 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 469 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 469 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 498 " 0.038 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN A 498 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 498 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 498 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 498 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" CG ASN A 498 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 498 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 498 " 0.012 2.00e-02 2.50e+03 ... (remaining 1934 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 313 2.70 - 3.25: 9310 3.25 - 3.80: 15472 3.80 - 4.35: 19189 4.35 - 4.90: 33322 Nonbonded interactions: 77606 Sorted by model distance: nonbonded pdb=" NZ LYS B 218 " pdb=" O SER B 219 " model vdw 2.149 3.120 nonbonded pdb=" N GLU B 55 " pdb=" OE1 GLU B 55 " model vdw 2.251 3.120 nonbonded pdb=" OG SER A 165 " pdb=" OG1 THR A 210 " model vdw 2.256 3.040 nonbonded pdb=" NH2 ARG A 464 " pdb=" OD2 ASP A 482 " model vdw 2.294 3.120 nonbonded pdb=" NH2 ARG A 355 " pdb=" O MET B 538 " model vdw 2.295 3.120 ... (remaining 77601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.090 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10878 Z= 0.148 Angle : 0.693 18.534 14835 Z= 0.334 Chirality : 0.049 0.753 1666 Planarity : 0.005 0.103 1930 Dihedral : 15.218 107.256 4183 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 0.18 % Allowed : 17.13 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1346 helix: None (None), residues: 0 sheet: 0.86 (0.20), residues: 657 loop : -0.82 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 73 HIS 0.008 0.001 HIS B 534 PHE 0.022 0.001 PHE A 173 TYR 0.014 0.001 TYR B 166 ARG 0.003 0.000 ARG B 506 Details of bonding type rmsd link_NAG-ASN : bond 0.01058 ( 7) link_NAG-ASN : angle 7.51686 ( 21) link_BETA1-4 : bond 0.00578 ( 5) link_BETA1-4 : angle 3.09671 ( 15) hydrogen bonds : bond 0.10743 ( 352) hydrogen bonds : angle 5.67333 ( 906) SS BOND : bond 0.00189 ( 12) SS BOND : angle 0.44012 ( 24) covalent geometry : bond 0.00324 (10854) covalent geometry : angle 0.62542 (14775) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 1.168 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.2451 time to fit residues: 21.3751 Evaluate side-chains 54 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 306 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 50.0000 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS B 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.188232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.170783 restraints weight = 17726.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.165966 restraints weight = 26271.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162738 restraints weight = 31315.225| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10878 Z= 0.194 Angle : 0.667 17.610 14835 Z= 0.327 Chirality : 0.047 0.652 1666 Planarity : 0.005 0.066 1930 Dihedral : 7.577 63.388 1721 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.02 % Favored : 93.83 % Rotamer: Outliers : 3.02 % Allowed : 15.62 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1346 helix: -5.43 (0.23), residues: 6 sheet: 0.80 (0.21), residues: 628 loop : -0.98 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 346 HIS 0.006 0.001 HIS B 534 PHE 0.029 0.002 PHE B 184 TYR 0.014 0.001 TYR A 109 ARG 0.002 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00975 ( 7) link_NAG-ASN : angle 6.52961 ( 21) link_BETA1-4 : bond 0.00530 ( 5) link_BETA1-4 : angle 2.60057 ( 15) hydrogen bonds : bond 0.03378 ( 352) hydrogen bonds : angle 5.30079 ( 906) SS BOND : bond 0.00233 ( 12) SS BOND : angle 0.68814 ( 24) covalent geometry : bond 0.00473 (10854) covalent geometry : angle 0.61567 (14775) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7540 (ppp) cc_final: 0.6969 (ppp) REVERT: A 346 TRP cc_start: 0.9238 (OUTLIER) cc_final: 0.8031 (m-10) REVERT: A 468 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8357 (m) REVERT: B 74 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8490 (ttpp) REVERT: B 152 MET cc_start: 0.7016 (tmm) cc_final: 0.6750 (tmm) outliers start: 34 outliers final: 18 residues processed: 87 average time/residue: 0.2356 time to fit residues: 30.5374 Evaluate side-chains 78 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 450 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 128 optimal weight: 7.9990 chunk 55 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 68 optimal weight: 50.0000 chunk 98 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.188807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.170994 restraints weight = 17874.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.165764 restraints weight = 26082.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.161925 restraints weight = 30138.690| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10878 Z= 0.143 Angle : 0.620 16.674 14835 Z= 0.303 Chirality : 0.046 0.618 1666 Planarity : 0.005 0.069 1930 Dihedral : 6.461 54.700 1720 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 3.28 % Allowed : 16.15 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.23), residues: 1346 helix: -5.42 (0.24), residues: 6 sheet: 0.84 (0.20), residues: 630 loop : -0.94 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 273 HIS 0.003 0.001 HIS B 146 PHE 0.022 0.002 PHE B 184 TYR 0.011 0.001 TYR B 405 ARG 0.002 0.000 ARG A 464 Details of bonding type rmsd link_NAG-ASN : bond 0.00990 ( 7) link_NAG-ASN : angle 5.91649 ( 21) link_BETA1-4 : bond 0.00536 ( 5) link_BETA1-4 : angle 2.32845 ( 15) hydrogen bonds : bond 0.03017 ( 352) hydrogen bonds : angle 5.05957 ( 906) SS BOND : bond 0.00203 ( 12) SS BOND : angle 0.50906 ( 24) covalent geometry : bond 0.00345 (10854) covalent geometry : angle 0.57431 (14775) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 64 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7537 (ppp) cc_final: 0.7095 (ppp) REVERT: A 468 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8346 (m) outliers start: 37 outliers final: 27 residues processed: 93 average time/residue: 0.2063 time to fit residues: 29.0090 Evaluate side-chains 85 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 38 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.191515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.174087 restraints weight = 17322.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.169728 restraints weight = 25607.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165101 restraints weight = 28989.829| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10878 Z= 0.114 Angle : 0.600 15.960 14835 Z= 0.293 Chirality : 0.045 0.608 1666 Planarity : 0.004 0.070 1930 Dihedral : 5.838 52.551 1720 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 3.19 % Allowed : 16.15 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.23), residues: 1346 helix: -5.41 (0.24), residues: 6 sheet: 0.88 (0.20), residues: 630 loop : -0.88 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 273 HIS 0.006 0.001 HIS B 146 PHE 0.028 0.001 PHE A 493 TYR 0.010 0.001 TYR B 405 ARG 0.002 0.000 ARG A 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 7) link_NAG-ASN : angle 5.45207 ( 21) link_BETA1-4 : bond 0.00369 ( 5) link_BETA1-4 : angle 2.21011 ( 15) hydrogen bonds : bond 0.02720 ( 352) hydrogen bonds : angle 4.87076 ( 906) SS BOND : bond 0.00205 ( 12) SS BOND : angle 0.43269 ( 24) covalent geometry : bond 0.00272 (10854) covalent geometry : angle 0.55989 (14775) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7578 (ppp) cc_final: 0.7257 (ppp) REVERT: A 135 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.5516 (m-10) REVERT: A 789 ARG cc_start: -0.1527 (OUTLIER) cc_final: -0.2413 (tmt170) REVERT: B 233 ASP cc_start: 0.5850 (OUTLIER) cc_final: 0.4963 (p0) outliers start: 36 outliers final: 25 residues processed: 88 average time/residue: 0.2072 time to fit residues: 27.8569 Evaluate side-chains 85 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 91 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 85 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.187310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.169584 restraints weight = 17549.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.164858 restraints weight = 25327.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.162664 restraints weight = 22640.829| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10878 Z= 0.184 Angle : 0.642 15.930 14835 Z= 0.316 Chirality : 0.047 0.627 1666 Planarity : 0.005 0.076 1930 Dihedral : 5.780 53.252 1720 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.79 % Favored : 94.13 % Rotamer: Outliers : 4.08 % Allowed : 16.15 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.23), residues: 1346 helix: -5.43 (0.23), residues: 6 sheet: 0.79 (0.20), residues: 629 loop : -0.97 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 273 HIS 0.004 0.001 HIS B 146 PHE 0.029 0.002 PHE A 493 TYR 0.013 0.001 TYR A 109 ARG 0.002 0.000 ARG A 506 Details of bonding type rmsd link_NAG-ASN : bond 0.00818 ( 7) link_NAG-ASN : angle 5.33310 ( 21) link_BETA1-4 : bond 0.00416 ( 5) link_BETA1-4 : angle 2.17737 ( 15) hydrogen bonds : bond 0.03307 ( 352) hydrogen bonds : angle 5.02765 ( 906) SS BOND : bond 0.00248 ( 12) SS BOND : angle 0.65808 ( 24) covalent geometry : bond 0.00450 (10854) covalent geometry : angle 0.60641 (14775) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 62 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.5704 (m-10) REVERT: A 789 ARG cc_start: -0.1448 (OUTLIER) cc_final: -0.2330 (tmt170) outliers start: 46 outliers final: 35 residues processed: 98 average time/residue: 0.1907 time to fit residues: 29.1656 Evaluate side-chains 94 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 133 optimal weight: 9.9990 chunk 5 optimal weight: 0.0980 chunk 121 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 119 optimal weight: 0.3980 chunk 130 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 0.0070 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.190071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.170233 restraints weight = 17694.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.166164 restraints weight = 31462.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.164076 restraints weight = 32878.020| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10878 Z= 0.099 Angle : 0.600 15.385 14835 Z= 0.292 Chirality : 0.045 0.588 1666 Planarity : 0.004 0.078 1930 Dihedral : 5.342 50.524 1720 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 3.28 % Allowed : 17.57 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.23), residues: 1346 helix: -5.43 (0.23), residues: 6 sheet: 0.88 (0.20), residues: 630 loop : -0.79 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 273 HIS 0.003 0.001 HIS B 146 PHE 0.030 0.001 PHE A 493 TYR 0.010 0.001 TYR B 405 ARG 0.003 0.000 ARG B 506 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 7) link_NAG-ASN : angle 4.96324 ( 21) link_BETA1-4 : bond 0.00425 ( 5) link_BETA1-4 : angle 2.15466 ( 15) hydrogen bonds : bond 0.02551 ( 352) hydrogen bonds : angle 4.72395 ( 906) SS BOND : bond 0.00186 ( 12) SS BOND : angle 0.38335 ( 24) covalent geometry : bond 0.00231 (10854) covalent geometry : angle 0.56693 (14775) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.5618 (m-10) REVERT: A 562 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7061 (ttt180) REVERT: A 789 ARG cc_start: -0.1463 (OUTLIER) cc_final: -0.2370 (tmt170) REVERT: B 233 ASP cc_start: 0.5832 (OUTLIER) cc_final: 0.4935 (p0) outliers start: 37 outliers final: 27 residues processed: 94 average time/residue: 0.2259 time to fit residues: 32.5988 Evaluate side-chains 92 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 114 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.188235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167113 restraints weight = 17823.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.162530 restraints weight = 34681.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.161174 restraints weight = 37132.721| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10878 Z= 0.155 Angle : 0.635 15.300 14835 Z= 0.309 Chirality : 0.045 0.608 1666 Planarity : 0.005 0.078 1930 Dihedral : 5.355 50.537 1720 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 3.99 % Allowed : 17.04 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1346 helix: -5.43 (0.23), residues: 6 sheet: 0.89 (0.20), residues: 634 loop : -0.80 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 273 HIS 0.002 0.001 HIS B 146 PHE 0.029 0.001 PHE A 493 TYR 0.011 0.001 TYR A 109 ARG 0.002 0.000 ARG A 789 Details of bonding type rmsd link_NAG-ASN : bond 0.00786 ( 7) link_NAG-ASN : angle 4.93711 ( 21) link_BETA1-4 : bond 0.00459 ( 5) link_BETA1-4 : angle 2.13471 ( 15) hydrogen bonds : bond 0.03048 ( 352) hydrogen bonds : angle 4.86222 ( 906) SS BOND : bond 0.00209 ( 12) SS BOND : angle 0.52080 ( 24) covalent geometry : bond 0.00380 (10854) covalent geometry : angle 0.60447 (14775) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 62 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5777 (m-10) REVERT: A 562 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7098 (ttt180) REVERT: A 789 ARG cc_start: -0.1359 (OUTLIER) cc_final: -0.2294 (tmt170) REVERT: B 233 ASP cc_start: 0.5842 (OUTLIER) cc_final: 0.4952 (p0) outliers start: 45 outliers final: 35 residues processed: 99 average time/residue: 0.2328 time to fit residues: 37.0900 Evaluate side-chains 99 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 74 optimal weight: 50.0000 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.187080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.165830 restraints weight = 17507.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161515 restraints weight = 34276.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159935 restraints weight = 35527.818| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10878 Z= 0.174 Angle : 0.648 15.336 14835 Z= 0.317 Chirality : 0.046 0.614 1666 Planarity : 0.005 0.081 1930 Dihedral : 5.306 51.177 1718 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 4.44 % Allowed : 16.24 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1346 helix: -5.43 (0.23), residues: 6 sheet: 0.94 (0.21), residues: 621 loop : -0.88 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 273 HIS 0.002 0.001 HIS B 146 PHE 0.018 0.002 PHE A 493 TYR 0.013 0.001 TYR A 109 ARG 0.002 0.000 ARG A 789 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 7) link_NAG-ASN : angle 4.91295 ( 21) link_BETA1-4 : bond 0.00420 ( 5) link_BETA1-4 : angle 2.16763 ( 15) hydrogen bonds : bond 0.03216 ( 352) hydrogen bonds : angle 4.96206 ( 906) SS BOND : bond 0.00220 ( 12) SS BOND : angle 0.59151 ( 24) covalent geometry : bond 0.00427 (10854) covalent geometry : angle 0.61820 (14775) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 62 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6356 (OUTLIER) cc_final: 0.6036 (m-10) REVERT: A 427 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 562 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7059 (ttt180) outliers start: 50 outliers final: 39 residues processed: 104 average time/residue: 0.2735 time to fit residues: 44.5721 Evaluate side-chains 98 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 56 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 101 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 131 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.187376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.166334 restraints weight = 17755.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.161740 restraints weight = 33480.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159924 restraints weight = 37451.780| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10878 Z= 0.157 Angle : 0.648 15.131 14835 Z= 0.316 Chirality : 0.046 0.603 1666 Planarity : 0.005 0.085 1930 Dihedral : 5.217 50.450 1718 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 4.08 % Allowed : 16.59 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1346 helix: -5.44 (0.23), residues: 6 sheet: 0.89 (0.20), residues: 630 loop : -0.85 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 273 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE B 173 TYR 0.011 0.001 TYR A 109 ARG 0.002 0.000 ARG B 506 Details of bonding type rmsd link_NAG-ASN : bond 0.00762 ( 7) link_NAG-ASN : angle 4.80911 ( 21) link_BETA1-4 : bond 0.00428 ( 5) link_BETA1-4 : angle 2.17657 ( 15) hydrogen bonds : bond 0.03043 ( 352) hydrogen bonds : angle 4.92118 ( 906) SS BOND : bond 0.00213 ( 12) SS BOND : angle 0.55316 ( 24) covalent geometry : bond 0.00387 (10854) covalent geometry : angle 0.61966 (14775) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 59 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6377 (OUTLIER) cc_final: 0.6062 (m-10) REVERT: A 427 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 562 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7099 (ttt180) outliers start: 46 outliers final: 40 residues processed: 99 average time/residue: 0.2546 time to fit residues: 38.4346 Evaluate side-chains 98 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 55 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 67 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.190729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170769 restraints weight = 17406.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.166968 restraints weight = 32509.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165533 restraints weight = 42010.275| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10878 Z= 0.115 Angle : 0.623 14.706 14835 Z= 0.302 Chirality : 0.045 0.581 1666 Planarity : 0.004 0.087 1930 Dihedral : 4.944 47.882 1718 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 3.19 % Allowed : 17.48 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1346 helix: -5.43 (0.24), residues: 6 sheet: 1.02 (0.21), residues: 625 loop : -0.75 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 273 HIS 0.005 0.001 HIS B 183 PHE 0.016 0.001 PHE A 549 TYR 0.010 0.001 TYR B 405 ARG 0.003 0.000 ARG B 506 Details of bonding type rmsd link_NAG-ASN : bond 0.00789 ( 7) link_NAG-ASN : angle 4.62947 ( 21) link_BETA1-4 : bond 0.00447 ( 5) link_BETA1-4 : angle 2.14741 ( 15) hydrogen bonds : bond 0.02609 ( 352) hydrogen bonds : angle 4.73388 ( 906) SS BOND : bond 0.00176 ( 12) SS BOND : angle 0.42216 ( 24) covalent geometry : bond 0.00280 (10854) covalent geometry : angle 0.59508 (14775) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5867 (m-10) REVERT: A 427 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8363 (mp) REVERT: A 562 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7098 (ttt180) outliers start: 36 outliers final: 33 residues processed: 86 average time/residue: 0.2448 time to fit residues: 32.9822 Evaluate side-chains 90 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 54 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 108 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 76 optimal weight: 30.0000 chunk 67 optimal weight: 0.0870 chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.185823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.164842 restraints weight = 17478.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.160443 restraints weight = 34510.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158253 restraints weight = 36808.308| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10878 Z= 0.244 Angle : 0.710 15.144 14835 Z= 0.350 Chirality : 0.047 0.618 1666 Planarity : 0.005 0.082 1930 Dihedral : 5.481 50.614 1718 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 93.98 % Rotamer: Outliers : 3.90 % Allowed : 16.86 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1346 helix: -5.45 (0.23), residues: 6 sheet: 0.83 (0.21), residues: 608 loop : -0.94 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 273 HIS 0.003 0.001 HIS B 183 PHE 0.029 0.002 PHE A 493 TYR 0.021 0.002 TYR A 109 ARG 0.004 0.000 ARG A 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00761 ( 7) link_NAG-ASN : angle 4.86281 ( 21) link_BETA1-4 : bond 0.00421 ( 5) link_BETA1-4 : angle 2.18745 ( 15) hydrogen bonds : bond 0.03692 ( 352) hydrogen bonds : angle 5.14493 ( 906) SS BOND : bond 0.00264 ( 12) SS BOND : angle 0.82734 ( 24) covalent geometry : bond 0.00601 (10854) covalent geometry : angle 0.68286 (14775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4523.89 seconds wall clock time: 84 minutes 31.69 seconds (5071.69 seconds total)